I think must have upgrades are things that are tougher to do after the house is built, wether it is phyiscally harder, or it looks better.
Things like:
raising ceilings on main and basement
widening garage
speaker wiring
extra exterior outlets/switches for lighting
outlet on island
rough in for garborator with switch on counter
drain in garage
finished basement stairs (that way they do a better job of the rough in)
upgrade railing (if you have stub walls)
vaulted ceilings
3 way switches where they do not exist
upgrade windows to more energy effiecient ones
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